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If you want an uncluttered desktop — but at-hand USB ports — embed a USB port right into your desk for at-your-fingertips access without the clutter of cables or a box sitting on your desktop.
Make magazine shares a tutorial for embedding a USB hub into your desk surface. They rely heavily on the Dremel Multi-Max oscillating tool — predominately because of Dremel's sponsorship of the project but also because it's a really handy all-in-one tool for the job — you could easily swap out other tools you have on hand (like a drill and jigsaw in place of the oscillating flush-cut wood blade). You're essentially cutting a hole the size of the USB hub's face, epoxying brackets onto the side of the hub, and screwing the brackets into the bottom of the desk so that the hub sits flush with the table surface.
Alternatively, steal an idea from my office makeover and mount your USB hub to the underside of your desk. Thanks rnpg1014!